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ORCIDJosé L. Medina-Franco
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Journal Articles
- 2024
[j44]Juan F. Avellaneda-Tamayo
, Ana L. Chávez-Hernández, Diana L. Prado-Romero, José L. Medina-Franco:
Chemical Multiverse and Diversity of Food Chemicals. J. Chem. Inf. Model. 64(4): 1229-1244 (2024)- [j43]Angel Jonathan Ruiz-Moreno, Raziel Cedillo-González, Luis Cordova-Bahena, Zhiqiang An, José L. Medina-Franco, Marco Velasco-Velázquez:
Consensus Pharmacophore Strategy For Identifying Novel SARS-Cov-2 Mpro Inhibitors from Large Chemical Libraries. J. Chem. Inf. Model. 64(6): 1984-1995 (2024) - [j42]Alejandro Gómez-García, Daniel A Acuña Jiménez, William J. Zamora, Haruna L. Barazorda-Ccahuana, Miguel Á. Chávez-Fumagalli, Marilia Valli, Adriano D. Andricopulo, Vanderlan da S. Bolzani, Dionisio A Olmedo, Pablo N. Solís, Marvin J. Núñez, Johny R. Rodríguez Pérez, Hoover A. Valencia Sánchez, Héctor F. Cortés Hernández, Oscar M. Mosquera Martinez, José L. Medina-Franco:
Latin American Natural Product Database (LANaPDB): An Update. J. Chem. Inf. Model. 64(22): 8495-8509 (2024) - 2023
- [j41]Karla Gonzalez-Ponce, Carolina Horta Andrade, Fiona M. I. Hunter, Johannes Kirchmair, Karina Martínez-Mayorga, José L. Medina-Franco, Matthias Rarey, Alexander Tropsha, Alexandre Varnek, Barbara Zdrazil:
School of cheminformatics in Latin America. J. Cheminformatics 15(1): 82 (2023) - [j40]Daniela Gaytán-Hernández, Ana L. Chávez-Hernández, Edgar López-López, Jazmín Miranda-Salas, Fernanda I. Saldívar-González, José L. Medina-Franco:
Art driven by visual representations of chemical space. J. Cheminformatics 15(1): 100 (2023) - 2022
- [j39]José L. Medina-Franco, Edgar López-López:
The Essence and Transcendence of Scientific Publishing. Frontiers Res. Metrics Anal. 7: 822453 (2022) - [j38]José L. Medina-Franco, Norberto Sánchez-Cruz, Edgar López-López, Bárbara I. Díaz-Eufracio:
Progress on open chemoinformatic tools for expanding and exploring the chemical space. J. Comput. Aided Mol. Des. 36(5): 341-354 (2022) - [j37]Veerabahu Shanmugasundaram, Jürgen Bajorath, Ralph E. Christoffersen, James D. Petke, W. Jeffrey Howe, Mark A. Johnson, Dimitris K. Agrafiotis, Pil Lee, Leslie A. Kuhn, Jay T. Goodwin, M. Katharine Holloway, Thompson N. Doman, W. Patrick Walters, Suzanne K. Schreyer, José L. Medina-Franco, Karina Martínez-Mayorga, Linda L. Restifo:
Epilogue to the Gerald Maggiora Festschrift: a tribute to an exemplary mentor, colleague, collaborator, and innovator. J. Comput. Aided Mol. Des. 36(9): 623-638 (2022) - [j36]Jürgen Bajorath, Ana L. Chávez-Hernández, Miquel Duran-Frigola, Eli Fernández-de Gortari, Johann Gasteiger, Edgar López-López, Gerald M. Maggiora, José L. Medina-Franco, Oscar Méndez-Lucio, Jordi Mestres, Ramón Alain Miranda-Quintana, Tudor I. Oprea, Fabien Plisson, Fernando D. Prieto-Martínez, Raquel Rodríguez-Pérez, Paola Rondón-Villarreal, Fernanda I. Saldívar-González, Norberto Sánchez-Cruz, Marilia Valli:
Chemoinformatics and artificial intelligence colloquium: progress and challenges in developing bioactive compounds. J. Cheminformatics 14(1): 82 (2022) - [j35]Timothy B. Dunn, Gustavo de M. Seabra, Taewon David Kim, K. Eurídice Juárez-Mercado, Chenglong Li, José L. Medina-Franco, Ramón Alain Miranda-Quintana:
Diversity and Chemical Library Networks of Large Data Sets. J. Chem. Inf. Model. 62(9): 2186-2201 (2022) - 2021
- [j34]Norberto Sánchez-Cruz, José L. Medina-Franco, Jordi Mestres, Xavier Barril:
Extended connectivity interaction features: improving binding affinity prediction through chemical description. Bioinform. 37(10): 1376-1382 (2021) - [j33]Fidele Ntie-Kang, Kiran K. Telukunta, Serge A. T. Fobofou, Victor Chukwudi Osamor, Samuel A. Egieyeh, Marilia Valli, Yannick Djoumbou Feunang, Maria Sorokina, Conrad Stork, Neann Mathai, Paul F. Zierep, Ana L. Chávez-Hernández, Miquel Duran-Frigola, Smith B. Babiaka, Romuald Tematio Fouedjou, Donatus B. Eni, Simeon Akame, Augustine B. Arreyetta-Bawak, Oyere T. Ebob, Jonathan A. Metuge, Boris D. Bekono, Mustafa A. Isa, Raphael Onuku, Daniel M. Shadrack, Thommas M. Musyoka, Vaishali M. Patil, Justin J. J. van der Hooft, Vanderlan da Silva Bolzani, José L. Medina-Franco, Johannes Kirchmair, Tilmann Weber, Özlem Tastan Bishop, Marnix H. Medema, Ludger A. Wessjohann, Jutta Ludwig-Müller:
Computational Applications in Secondary Metabolite Discovery (CAiSMD): an online workshop. J. Cheminformatics 13(1): 64 (2021) - [j32]Edgar López-López, Jürgen Bajorath, José L. Medina-Franco:
Informatics for Chemistry, Biology, and Biomedical Sciences. J. Chem. Inf. Model. 61(1): 26-35 (2021) - [j31]Norberto Sánchez-Cruz, José L. Medina-Franco:
Epigenetic Target Profiler: A Web Server to Predict Epigenetic Targets of Small Molecules. J. Chem. Inf. Model. 61(4): 1550-1554 (2021) - 2020
- [j30]Edgar López-López, Obdulia Rabal, Julen Oyarzabal, José L. Medina-Franco:
Towards the understanding of the activity of G9a inhibitors: an activity landscape and molecular modeling approach. J. Comput. Aided Mol. Des. 34(6): 659-669 (2020) - [j29]Fernanda I. Saldívar-González, C. Sebastian Huerta-García, José L. Medina-Franco:
Chemoinformatics-based enumeration of chemical libraries: a tutorial. J. Cheminformatics 12(1): 64 (2020) - [j28]Gerald M. Maggiora, José L. Medina-Franco, Javed Iqbal, Martin Vogt, Jürgen Bajorath:
From Qualitative to Quantitative Analysis of Activity and Property Landscapes. J. Chem. Inf. Model. 60(12): 5873-5880 (2020) - 2019
- [j27]J. Jesús Naveja, B. Angélica Pilón-Jiménez, Jürgen Bajorath, José L. Medina-Franco:
A general approach for retrosynthetic molecular core analysis. J. Cheminformatics 11(1): 61:1-61:9 (2019) - [j26]Fernanda I. Saldívar-González, Marilia Valli, Adriano D. Andricopulo, Vanderlan da Silva Bolzani, José L. Medina-Franco:
Chemical Space and Diversity of the NuBBE Database: A Chemoinformatic Characterization. J. Chem. Inf. Model. 59(1): 74-85 (2019) - [j25]J. Jesús Naveja, Dagmar Stumpfe, José L. Medina-Franco, Jürgen Bajorath:
Exploration of Target Synergy in Cancer Treatment by Cell-Based Screening Assay and Network Propagation Analysis. J. Chem. Inf. Model. 59(6): 3072-3079 (2019) - 2018
- [j24]Norberto Sánchez-Cruz, José L. Medina-Franco:
Statistical-based database fingerprint: chemical space dependent representation of compound databases. J. Cheminformatics 10(1): 55:1-55:13 (2018) - 2017
- [j23]Eli Fernández-de Gortari, César R. García-Jacas, Karina Martínez-Mayorga, José L. Medina-Franco:
Database fingerprint (DFP): an approach to represent molecular databases. J. Cheminformatics 9(1): 9:1-9:9 (2017) - [j22]Mariana González-Medina, Oscar Méndez-Lucio, José L. Medina-Franco:
Activity Landscape Plotter: A Web-Based Application for the Analysis of Structure-Activity Relationships. J. Chem. Inf. Model. 57(3): 397-402 (2017) - [j21]Mariana González-Medina, José L. Medina-Franco:
Platform for Unified Molecular Analysis: PUMA. J. Chem. Inf. Model. 57(8): 1735-1740 (2017) - 2016
- [j20]Mariana González-Medina, Fernando D. Prieto-Martínez, John R. Owen, José L. Medina-Franco:
Consensus Diversity Plots: a global diversity analysis of chemical libraries. J. Cheminformatics 8(1): 63:1-63:11 (2016) - 2015
- [j19]Oscar Méndez-Lucio, Albert J. Kooistra, Chris de Graaf, Andreas Bender, José L. Medina-Franco:
Analyzing Multitarget Activity Landscapes Using Protein-Ligand Interaction Fingerprints: Interaction Cliffs. J. Chem. Inf. Model. 55(2): 251-262 (2015) - [j18]Rosa L. Camacho-Mendoza, Evelin Gutiérrez-Moreno, Edmundo Guzmán-Percástegui, Eliazar Aquino-Torres, Julián Cruz-Borbolla, José A. Rodríguez-Ávila, José G. Alvarado-Rodríguez, Oscar Olvera-Neria, Pandiyan Thangarasu, José L. Medina-Franco:
Density Functional Theory and Electrochemical Studies: Structure-Efficiency Relationship on Corrosion Inhibition. J. Chem. Inf. Model. 55(11): 2391-2402 (2015) - 2014
- [j17]Rajarshi Guha, José L. Medina-Franco:
On the validity versus utility of activity landscapes: are all activity cliffs statistically significant? J. Cheminformatics 6(1): 11 (2014) - 2013
- [j16]José L. Medina-Franco, Bruce S. Edwards, Clemencia Pinilla, Jon R. Appel, Marc A. Giulianotti, Radleigh Santos, Austin B. Yongye, Larry A. Sklar, Richard A. Houghten:
Rapid Scanning Structure-Activity Relationships in Combinatorial Data Sets: Identification of Activity Switches. J. Chem. Inf. Model. 53(6): 1475-1485 (2013) - [j15]Radleigh Santos, Marc A. Giulianotti, Richard A. Houghten, José L. Medina-Franco:
Conditional Probabilistic Analysis for Prediction of the Activity Landscape and Relative Compound Activities. J. Chem. Inf. Model. 53(10): 2613-2625 (2013) - 2012
- [j14]José L. Medina-Franco, Austin B. Yongye, Jaime Pérez-Villanueva, Richard A. Houghten, Karina Martínez-Mayorga:
Activity-difference maps and consensus similarity measure characterize structure-activity relationships. J. Cheminformatics 4(S-1): 24 (2012) - [j13]Jakyung Yoo, José L. Medina-Franco:
Computer-guided discovery of epigenetics drugs: molecular modeling and identification of inhibitors of DNMT1. J. Cheminformatics 4(S-1): 25 (2012) - [j12]Fabian López-Vallejo, Jacob Waddell, Austin B. Yongye, Richard A. Houghten, José L. Medina-Franco:
A large scale classification of molecular fingerprints for the chemical space representation and SAR analysis. J. Cheminformatics 4(S-1): 26 (2012) - [j11]Thomas Scior, Andreas Bender, Gary Tresadern, José L. Medina-Franco, Karina Martínez-Mayorga, Thierry Langer, Karina Cuanalo-Contreras, Dimitris K. Agrafiotis:
Recognizing Pitfalls in Virtual Screening: A Critical Review. J. Chem. Inf. Model. 52(4): 867-881 (2012) - [j10]Austin B. Yongye, José L. Medina-Franco:
Data Mining of Protein-Binding Profiling Data Identifies Structural Modifications that Distinguish Selective and Promiscuous Compounds. J. Chem. Inf. Model. 52(9): 2454-2461 (2012) - [j9]José L. Medina-Franco:
Scanning Structure-Activity Relationships with Structure-Activity Similarity and Related Maps: From Consensus Activity Cliffs to Selectivity Switches. J. Chem. Inf. Model. 52(10): 2485-2493 (2012) - 2011
- [j8]Jakyung Yoo, José L. Medina-Franco:
Homology modeling, docking and structure-based pharmacophore of inhibitors of DNA methyltransferase. J. Comput. Aided Mol. Des. 25(6): 555-567 (2011) - [j7]Austin B. Yongye, Kendall G. Byler, Radleigh Santos, Karina Martínez-Mayorga, Gerald M. Maggiora, José L. Medina-Franco:
Consensus Models of Activity Landscapes with Multiple Chemical, Conformer, and Property Representations. J. Chem. Inf. Model. 51(6): 1259-1270 (2011) - [j6]John R. Owen, Ian T. Nabney, José L. Medina-Franco, Fabian López-Vallejo:
Visualization of Molecular Fingerprints. J. Chem. Inf. Model. 51(7): 1552-1563 (2011) - [j5]José L. Medina-Franco, Austin B. Yongye, Jaime Pérez-Villanueva, Richard A. Houghten, Karina Martínez-Mayorga:
Multitarget Structure-Activity Relationships Characterized by Activity-Difference Maps and Consensus Similarity Measure. J. Chem. Inf. Model. 51(9): 2427-2439 (2011) - 2009
- [j4]José L. Medina-Franco, Karina Martínez-Mayorga, Andreas Bender, Ray M. Marín, Marc A. Giulianotti, Clemencia Pinilla, Richard A. Houghten:
Characterization of Activity Landscapes Using 2D and 3D Similarity Methods: Consensus Activity Cliffs. J. Chem. Inf. Model. 49(2): 477-491 (2009) - [j3]Narender Singh, Rajarshi Guha, Marc A. Giulianotti, Clemencia Pinilla, Richard A. Houghten, José L. Medina-Franco:
Chemoinformatic Analysis of Combinatorial Libraries, Drugs, Natural Products, and Molecular Libraries Small Molecule Repository. J. Chem. Inf. Model. 49(4): 1010-1024 (2009) - 2005
- [j2]José L. Medina-Franco, Alexander Golbraikh, Scott Oloff, Rafael Castillo, Alexander Tropsha:
Quantitative Structure-activity Relationship Analysis of Pyridinone HIV-1 Reverse Transcriptase Inhibitors using the k Nearest Neighbor Method and QSAR-based Database Mining. J. Comput. Aided Mol. Des. 19(4): 229-242 (2005) - 2004
- [j1]José L. Medina-Franco, Sergio Rodríguez-Morales, Cecilia Juárez-Gordiano, Alicia Hernández-Campos, Rafael Castillo:
Docking-based CoMFA and CoMSIA studies of non-nucleoside reverse transcriptase inhibitors of the pyridinone derivative type. J. Comput. Aided Mol. Des. 18(5): 345-360 (2004)
Informal and Other Publications
- 2021
- [i4]José L. Medina-Franco:
Expanding the Chemical Information Science gateway. F1000Research 10: 294 (2021) - [i3]José L. Medina-Franco, Karina Martínez-Mayorga, Eli Fernández-de Gortari, Johannes Kirchmair, Jürgen Bajorath:
Rationality over fashion and hype in drug design. F1000Research 10: 397 (2021) - 2018
- [i2]J. Jesús Naveja, Mariel P. Rico-Hidalgo, José L. Medina-Franco:
Analysis of a large food chemical database: chemical space, diversity, and complexity. F1000Research 7: 993 (2018) - 2017
- [i1]J. Jesús Naveja, José L. Medina-Franco:
ChemMaps: Towards an approach for visualizing the chemical space based on adaptive satellite compounds. F1000Research 6: 1134- (2017)
Coauthor Index
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